Background: 22q11.2 deletion syndrome (22q11DS) is associated with intellectual disability, poor social interaction and a high prevalence of psychosis. However, to date there have been no studies comparing cognition and neuroanatomical characteristics of 22q11DS with other syndromes to investigate if the cognitive strengths and difficulties and neuroanatomical differences associated with 22q11DS are specific to the syndrome. Hence, it is difficult to know if the observed features of 22q11DS are simply due to a non-specific effect of having a genetic disorder or are specific to 22q11DS. Methods: In this study, cognition and brain anatomy of 12 children with 22q11DS were compared to 12 age, gender and full scale IQ (FSIQ) matched children with William syndrome (WS) in order to investigate which cognitive and neuroanatomical features are specific to 22q11DS. We chose WS since the literature suggests that both groups have areas of physical/cognitive/behavioural overlap but as yet there has been no direct comparison of the two groups. Results: Despite being matched on FSIQ the WS group had significantly greater impairment than those with 22q11DS on tests of Performance IQ, while performing significantly better on tasks measuring verbal, social and facial processing skills. Moreover there were significant differences in brain anatomy. Despite similar overall brain volumes, midline anomalies were more common among the 22q11DS group, and regional differences such as increased striatal volumes and reduced cerebellar volumes in the 22q11DS group were detected. Conclusions: These findings suggest that although the behavioural phenotype is similar in some aspects there are key differences in cognition and neuroanatomy between the two groups. Different neuropsychological profiles need to be considered when designing educational frameworks for working with these children.